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hostedbymap #136

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claudio.atzori merged 60 commits from hostedbymap into beta 2021-08-12 17:10:55 +02:00
Conversation 1 Commits 60 Files Changed 46 +99 -7
1 changed files with 99 additions and 7 deletions
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106
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml
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@ -9,6 +9,10 @@
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>hostedByMapPath</name>
<description>the output path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -65,23 +69,30 @@
</configuration>
</global>
<start to="reset_outputpath"/>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="remove_hbmpath">${wf:conf('resumeFrom') eq 'ProduceHBM'}</case>
<default to="prepareInfo"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset_outputpath">
<action name="remove_hbmpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
<delete path="${hostedByMapPath}"/>
<!-- <mkdir path="${hostedByMapPath}"/>-->
</fs>
<ok to="fork_downloads_csv"/>
<error to="Kill"/>
</action>
<fork name="fork_downloads_csv">
<path start="download_gold"/>
<path start="download_doaj"/>
@ -134,13 +145,94 @@
</spark-opts>
<arg>--datasourcePath</arg><arg>${sourcePath}/datasource</arg>
<arg>--workingPath</arg><arg>${workingDir}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--outputPath</arg><arg>${hostedByMapPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<ok to="prepareInfo"/>
<error to="Kill"/>
</action>
<action name="prepareInfo">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<name>Prepare info to apply the hbm</name>
<class>eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--graphPath</arg><arg>${sourcePath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="fork_apply"/>
<error to="Kill"/>
</action>
<fork name="fork_apply">
<path start="apply_result"/>
<path start="apply_datasource"/>
</fork>
<action name="apply_result">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<name>Apply hbm to result</name>
<class>eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--graphPath</arg><arg>${sourcePath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="join_apply"/>
<error to="Kill"/>
</action>
<action name="apply_datasource">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<name>Apply hbm to datasource</name>
<class>eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToDatasource</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--outputPath</arg><arg>${outputPath}/datasource</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--graphPath</arg><arg>${sourcePath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="join_apply"/>
<error to="Kill"/>
</action>
<join name="join_apply" to="End"/>
<end name="End"/>